IncAAM 1.9

Summary presentation and defaults

• Removed the note column from fit$summary and changed both existing plot subtitles to display TR median instead of the TR threshold; the ogive plot no longer labels the same estimate as Median A50.
• Simplified fit$summary by removing p5, p95, and n_posterior_draws; retained CrI95_low and CrI95_high and the posterior SD. The draw counts remain available in ogive metadata.
• Updated default female and male TR thresholds to 0.16 and 0.25, respectively. Users may still override them with explicit arguments.
• Corrected the in-press methodological reference year to 2027 in the package documentation.

Changes to posterior estimation

• Replaced the version 1.8 population estimate based on aggregates of fish-level TR values with the hierarchical population median TR from the population log(c) intercept, using all post-warmup posterior draws.
• Removed the last-observed-increment censoring from fish-level TR draws and retained the posterior probability of crossing within the original observed range (TR_reached_prob) solely as a diagnostic.
• Reported 95% Bayesian credible intervals (posterior 2.5th–97.5th percentiles) for the hierarchical population estimates.
• Revised the group-level jerk estimate to the jerk of the hierarchical reference curve, clearly distinguished from fish-level diagnostic jerk summaries.

Analytical crossing ogive

• Replaced the logistic approximation based on averaged fish-level probabilities with the analytical hierarchical posterior crossing ogive from log(c) population intercept and fish-level SD posterior draws.
• Defined the estimated ogive A50 as the hierarchical population median TR; the ogive A50 now has a 95% Bayesian credible interval.
• Added posterior-median crossing probabilities and both 90% and 95% Bayesian credible limits to the ogive tables.

Increment selection

• Added min_max_incnum to select fish based on their original maximum observed increment (default NULL, no restriction).
• Added max_incnum_fit to cap the increment numbers used in the growth-curve likelihood (default Inf, no cap).
• Preserved the original observed increment maximum for threshold-reach diagnostics, even when only early increments are used in the fit. The pre-existing min_increments threshold is evaluated on the capped fitting sequence.

Output and documentation

• Updated the group summary and ogive tables to identify hierarchical estimands and posterior intervals; retained original result component names.
• Reformatted the existing TR/Jerk density plot and crossing-ogive plot. The ogive now uses 90% posterior credible shading rather than SE bars; no additional plot types were introduced.
• Updated README.md, function help, and package description for version 1.9.

IncAAM 1.8

• Previous submitted version. Fish-level TR estimates were truncated at each fish’s last observed increment; group summaries and a fitted logistic crossing ogive were derived from aggregated fish-level results.